Skip to content

okabe-lab/Watershed

Repository files navigation

Matlab scripts and Fiji macro for analyzing images of cleared cochlea immunostained with anti-MYO7A antibody using 3D watershed method.


This program needs:

Data size: Total 48 MB - Program 6 KB - Test data 48 MB


For testing the program, please run the scripts/macro as follows:

  1. Run "Watershed_main1.m" on Matlab, which calculates threshold value.
  2. Open "Watershed_main2 (macro for Fiji).txt".
  3. Make sure that "threshold" value in line 2 is the same as the value calculated in step 1.
  4. Close "Watershed_main2 (macro for Fiji).txt".
  5. Start Fiji and open "linearizedIm2.tif".
  6. Run "Watershed_main2 (macro for Fiji).txt" on Fiji.
  7. Save resulting "watershed.tif" file.
  8. Run "Watershed_main3.m" on Matlab.

It takes ~5 minutes for running all the scripts on PC with: Windows 10 Home, Inter Core i7-6700 CPU @ 3.40GHz, 16.0GB RAM.

Following result files will be saved in "..\Results":

  • "innerImage.tif", "outerImage.tif" (Images indicating detected cells)
  • "detectedHairCells.xlsx" (Coordinates of detected cells; sheet1:IHCs, sheet2:OHCs)

October 30, 2018

Tadatsune Iida Department of Cellular Neurobiology, Graduate School of Medicine, University of Tokyo Email: tadiida@m.u-tokyo.ac.jp

Shigeo Okabe Department of Cellular Neurobiology, Graduate School of Medicine, University of Tokyo Email: okabe@m.u-tokyo.ac.jp

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages